title: MPRA from K562 (ENCLB995JCM)

description:
https://www.encodeproject.org/experiments/ENCSR363XER/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR363XER
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR830AFA
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB995JCM
fragmentation methods: none

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS761XYS at ENCODE; https://www.encodeproject.org/ENCBS761XYS/


title: HA_dTAG_Serum30_Replicate2

status: Public on May 07 2024

type: SRA

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

country: USA

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
raw fastq data files were ran through fastqc/0.11.8 and low quality reads/adapter contamination were removed using trimgalore/0.6.4
Reads were mapped to the hg38 human reference genome using bowtie2/2.4.2. Reads were also mapped to the dm6 Drosophila genome to extract reads originating from the spike-ins chromatin for normalization purposes.
Duplicates were marked and removed using picard/2.10.3 and then files were sorted and indexed using samtools/1.6 in preparation for Bigwig generation.
Normalized BigWigs were made from sorted bam files using Deeptools command bamCoverage using either CPM normalization or scale factors generated from sorted Drosophila bam files.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: All cell lines were maintained in DMEM supplemented with 7% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in humidified atmosphere with 5% CO2 at 37C. For treatments, cells were placed in serum-free media for 48 hr prior to serum treatment for the corresponding time point. 8 hr prior to serum treatment, cells were pre-incubated with DMSO (vehicle control) or dTAG to induce KAP1 depletion.

extract_protocol:
For each ChIP, 1 x 15-cm tissue culture dish (yielding ~30E6 cells/plate) was utilized and seeded according to the experimental design in each figure (DMSO/dTAG +/- serum at different time points), and 20E6 cells were utilized per ChIP. For all Pol II ChIPs, cells were crosslinked with 0.5% methanol-free formaldehyde (Thermo Fisher Scientific, 28908) by adding directly to the dish in media at room temperature for 10 min with rocking and neutralization with 150 mM glycine for 5 min with rocking. For the ChIPs including HA (KAP1), SPT5, CDK9, TFIIB, MED1, and CDK7, 1% formaldehyde for 10 min was used instead of 0.5%. For all experiments, the media was removed and cells were washed twice with cold 1X PBS, cold PBS was added and then cells were scraped off the plate. Cells were centrifuged (1000xg, 5 min, 4°C), and pelleted, flash frozen in liquid nitrogen, and frozen at -80°C until ready to use. To perform the ChIP, cells were resuspended in 2 mL/dish of Farnham Lysis Buffer (5 mM PIPES pH = 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X Protease Inhibitor (RPI, catalog P50900-1)), counted by hemacytometer, resuspended to 10E6 cells/mL, nutated for 30 min at 4°C, and then centrifuged to isolate nuclei (1000xg, 5 min, 4°C). The supernatant was removed and nuclei resuspended in Szak’s RIPA Buffer (50 mM Tris-HCl pH = 8.0, 1% NP-40, 150 mM NaCl, 0.5% Na-Deoxycholate, 0.1% SDS, 2.5 mM EDTA pH = 8.0, 1 mM PMSF, and 1X Protease Inhibitor) at a concentration of 25E6 nuclei/mL.
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems, catalog KK8502) following the manufacturers protocol.

tag: cell line

tag: genotype


title: HA_dTAG_Serum30_Replicate1


title: HA_DMSO_Serum180_Replicate2


title: MPRA from K562 (ENCLB564GCS)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR274WZF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR274WZF
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB564GCS
fragmentation methods: none

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: Sex

value: female

tag: health state

tag: dev stage

value: adult

tag: age

tag: passage number

tag: lab

value: Ryan Tewhey, JAX

tag: source

value: ATCC

tag: link

value: ENCBS656EPZ at ENCODE; https://www.encodeproject.org/ENCBS656EPZ/


title: HA_DMSO_Serum180_Replicate1


title: MPRA from K562 (ENCLB971AYS)

description:
https://www.encodeproject.org/experiments/ENCSR274WZF/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR274WZF
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB971AYS
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: ENCBS103OBV at ENCODE; https://www.encodeproject.org/ENCBS103OBV/


title: MPRA from K562 (ENCLB347XVP)

description:
https://www.encodeproject.org/experiments/ENCSR341GVP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR341GVP
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB347XVP
fragmentation methods: none

value: ENCBS346WSM at ENCODE; https://www.encodeproject.org/ENCBS346WSM/


title: MPRA from K562 (ENCLB037UOE)

description:
https://www.encodeproject.org/experiments/ENCSR341GVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341GVP
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB037UOE
fragmentation methods: none

value: ENCBS591PHZ at ENCODE; https://www.encodeproject.org/ENCBS591PHZ/


title: MPRA from K562 (ENCLB428QSX)

description:
https://www.encodeproject.org/experiments/ENCSR274WZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR274WZF
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB428QSX
fragmentation methods: none

value: ENCBS770SAY at ENCODE; https://www.encodeproject.org/ENCBS770SAY/


title: HA_DMSO_Serum30_Replicate2


title: HA_DMSO_Serum30_Replicate1


title: MPRA from K562 (ENCLB657WKY)

description:
https://www.encodeproject.org/experiments/ENCSR274WZF/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR274WZF
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB657WKY
fragmentation methods: none

value: ENCBS606SPP at ENCODE; https://www.encodeproject.org/ENCBS606SPP/


title: PolII_Ser2P_DMSO_Serum30_Replicate2


title: PolII_Ser2P_DMSO_Serum30_Replicate1


title: MPRA from K562 (ENCLB610PNK)

description:
https://www.encodeproject.org/experiments/ENCSR274WZF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR274WZF
assay title: MPRA
possible controls: ENCSR441MQR
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB610PNK
fragmentation methods: none

value: ENCBS226IBK at ENCODE; https://www.encodeproject.org/ENCBS226IBK/


title: PolII_dTAG_Serum30_Replicate2


title: MPRA from A549 (ENCLB754DAQ)

description:
https://www.encodeproject.org/experiments/ENCSR273YGD/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR273YGD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR738NIX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB754DAQ
fragmentation methods: none

source_name: Homo sapiens A549 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: male

value: 58 years

value: ENCBS308MZC at ENCODE; https://www.encodeproject.org/ENCBS308MZC/


title: MPRA from A549 (ENCLB142MRS)

description:
https://www.encodeproject.org/experiments/ENCSR273YGD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR273YGD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR738NIX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB142MRS
fragmentation methods: none

value: ENCBS103NBF at ENCODE; https://www.encodeproject.org/ENCBS103NBF/


title: MPRA from A549 (ENCLB211MBC)

description:
https://www.encodeproject.org/experiments/ENCSR273YGD/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR273YGD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR738NIX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB211MBC
fragmentation methods: none

value: cell line

value: ENCBS504VRU at ENCODE; https://www.encodeproject.org/ENCBS504VRU/


title: MPRA from K562 (ENCLB395NVZ)

description:
https://www.encodeproject.org/experiments/ENCSR341GVP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR341GVP
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB395NVZ
fragmentation methods: none

value: not applicable

value: female

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS749LMV at ENCODE; https://www.encodeproject.org/ENCBS749LMV/


title: PolII_DMSO_Serum30_Replicate1


title: HA_DMSO_Serum0_Replicate2


title: PolII_dTAG_Serum15_Replicate2


title: PolII_dTAG_Serum15_Replicate1


title: PolII_DMSO_Serum15_Replicate1


title: MPRA from GM12878 (ENCLB133AFW)

description:
https://www.encodeproject.org/experiments/ENCSR248ZDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZDI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB133AFW
fragmentation methods: none

source_name: Homo sapiens GM12878 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: unknown

value: adult

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS474WBG at ENCODE; https://www.encodeproject.org/ENCBS474WBG/


title: PolII_dTAG_Serum0_Replicate1


title: MPRA from A549 (ENCLB989ZUW)

description:
https://www.encodeproject.org/experiments/ENCSR273YGD/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR273YGD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR738NIX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB989ZUW
fragmentation methods: none

value: ENCBS930EUC at ENCODE; https://www.encodeproject.org/ENCBS930EUC/


title: PolII_dTAG_Serum0_Replicate2


title: MPRA from GM12878 (ENCLB221ELB)

description:
https://www.encodeproject.org/experiments/ENCSR248ZDI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZDI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB221ELB
fragmentation methods: none

value: ENCBS147UFA at ENCODE; https://www.encodeproject.org/ENCBS147UFA/


title: PolII_DMSO_Serum30_Replicate2


title: MPRA from Jurkat (ENCLB698BVY)

description:
https://www.encodeproject.org/experiments/ENCSR247RPW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR247RPW
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB698BVY
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens Jurkat cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

value: Jurkat

value: male

value: acute T cell leukemia

value: child

value: 14 years

value: ENCBS047PVV at ENCODE; https://www.encodeproject.org/ENCBS047PVV/


title: MPRA from GM12878 (ENCLB725OJY)

description:
https://www.encodeproject.org/experiments/ENCSR248ZDI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZDI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB725OJY
fragmentation methods: none

value: cell line

value: not applicable

value: female

value: ENCBS343DEI at ENCODE; https://www.encodeproject.org/ENCBS343DEI/


title: PolII_DMSO_Serum15_Replicate2


title: MPRA from A549 (ENCLB480SGR)

description:
https://www.encodeproject.org/experiments/ENCSR213UGS/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR213UGS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR205HWY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB480SGR
fragmentation methods: none

value: 58 years

value: ENCBS906VDW at ENCODE; https://www.encodeproject.org/ENCBS906VDW/


title: HA_DMSO_Serum0_Replicate1


title: ExVi2Red_01_A01

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

library_source: transcriptomic single cell

data_processing:
Raw reads in fastq format were trimmed using trim-galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome, GRCz10, using HISAT2 with default parameters. htseq-count was used to assign reads to exons thus eventually getting counts per gene.
For analysis, cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non-responsive were compared using ROTS with default parameters.  Genes with false-discovery rate (FDR) less than 0.05 were considered as differentially expressed.
For gene ontology (GO) analysis of differentially expressed genes, FishEnrichR was utilized.  As background, genes expressed in at least 5 % of the cells were used.
Assembly: GRCz10
Supplementary files format and content: csv

molecule: polyA RNA

organism: Danio rerio

source_name: pancreas

growth_protocol: 4 months old Tg(ins:CaMPARI) zebrafish

extract_protocol:
The photoconverted islets were dissociated into single cells by incubation in TrypLE (ThermoFisher, 12563029) at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation, TrypLE was inactivated with 10% FBS, and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded, and the pellet re-suspended in 500 µl of HBSS (without Ca2+, Mg2+).  To remove debris, the solution was passed over a 30 µm cell filter (Miltenyi Biotec, 130-041-407).  To remove dead cells, calcein violet (ThermoFisher, C34858) was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC (Fluorescein isothiocyanate) for green fluorescence; and PE (Phycoerythrin) for red fluorescence.
For single-cell RNA-Seq, β-cells isolated from Tg(ins:CaMPARI) islets were subjected to profiling using Smart-Seq2 protocol from Takara.  For this, islets were isolated, photoconverted ex vivo, dissociated and FAC-sorted as described above.  β-cells were collected from two conditions: responsive β-cells displaying photoconversion at 2.5 mM; and non-responsive β-cells without photoconversion at 16.5 mM.  Photoconversion was defined as a high red-to-green ratio.  For FACS of each condition, index sorting was utilized, and the cells were collected in 96-well plate containing lysis buffer (2 µl of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB)).  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication (Singh et al., Scientific Reports, 2018; doi: 10.1038/s41598-018-35218-5).
Smart-Seq2 from Takara

treatment_protocol: The primary islets from 4 months post-fertilization Tg(ins:CaMPARI) animals were dissected from the fish after euthanasia.  Each islet was placed in a well of 24-well plate with 5 ml of DPBS medium supplemented with calcium, magnesium (ThermoFisher, 14040141), along with the appropriate concentration of D-Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently, the entire 24-well plate was photoconverted using a 405 nm LED array (Loctite, 1167593) for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller (Loctite, 1359255) was utilized for precise timing of light exposure.

tag: tissue

value: pancreas

value: 4 mpf

tag: cell type

value: beta-cell

tag: treatment

value: photoconversion


title: PolII_DMSO_Serum0_Replicate1

tag: cell line

tag: genotype


title: MPRA from A549 (ENCLB546JJB)

description:
https://www.encodeproject.org/experiments/ENCSR273YGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273YGD
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR738NIX
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB546JJB
fragmentation methods: none

tag: line

tag: biosample encode accession

value: adult

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS446NYP at ENCODE; https://www.encodeproject.org/ENCBS446NYP/


title: PolII_dTAG_Serum30_Replicate1


title: MPRA from A549 (ENCLB966PAR)

description:
https://www.encodeproject.org/experiments/ENCSR213UGS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR213UGS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR205HWY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB966PAR
fragmentation methods: none

tag: collection date

tag: geographic location

value: male

value: ENCBS229WEX at ENCODE; https://www.encodeproject.org/ENCBS229WEX/


title: ExVi2Red_01_B01


title: ExVi2Red_01_D01


title: MPRA from GM12878 (ENCLB831DBH)

description:
https://www.encodeproject.org/experiments/ENCSR248ZDI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZDI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB831DBH
fragmentation methods: none

tag: encode accession

tag: Sex

value: unknown

value: ENCBS621PNO at ENCODE; https://www.encodeproject.org/ENCBS621PNO/


title: MPRA from A549 (ENCLB062NHS)

description:
https://www.encodeproject.org/experiments/ENCSR213UGS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR213UGS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR205HWY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB062NHS
fragmentation methods: none

value: cell line

value: not applicable

tag: dev stage

value: ENCBS668VBH at ENCODE; https://www.encodeproject.org/ENCBS668VBH/


title: ExVi2Red_01_C01

tag: age


title: MPRA from SK-N-SH (ENCLB310HKL)

description:
https://www.encodeproject.org/experiments/ENCSR181PJG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR181PJG
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB310HKL
fragmentation methods: none

source_name: Homo sapiens SK-N-SH cell line genetically modified (episome) using transient transfection

value: SK-N-SH

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 years

value: ENCBS208PMU at ENCODE; https://www.encodeproject.org/ENCBS208PMU/


title: PolII_DMSO_Serum0_Replicate2


title: MPRA from SK-N-SH (ENCLB346HBD)

description:
https://www.encodeproject.org/experiments/ENCSR181PJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181PJG
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB346HBD
fragmentation methods: none

tag: lab

value: ENCBS179LMB at ENCODE; https://www.encodeproject.org/ENCBS179LMB/


title: ExVi2Red_01_F01

value: pancreas

value: 4 mpf

value: beta-cell

value: photoconversion


title: ExVi2Red_01_E01


title: MPRA from SK-N-SH (ENCLB265GNA)

description:
https://www.encodeproject.org/experiments/ENCSR181PJG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR181PJG
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB265GNA
fragmentation methods: none

value: Ryan Tewhey, JAX

tag: source

value: ATCC

value: ENCBS977BRF at ENCODE; https://www.encodeproject.org/ENCBS977BRF/


title: MPRA from SK-N-SH (ENCLB437GQQ)

description:
https://www.encodeproject.org/experiments/ENCSR181PJG/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR181PJG
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB437GQQ
fragmentation methods: none

value: cell line

tag: link

value: ENCBS730EAI at ENCODE; https://www.encodeproject.org/ENCBS730EAI/


title: ExVi2Red_01_G01

tag: tissue


title: ExVi2Red_01_H01

tag: cell type


title: MPRA from HepG2 (ENCLB486RCU)

description:
https://www.encodeproject.org/experiments/ENCSR167HAR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR167HAR
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB486RCU
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: not applicable

value: male

value: hepatocellular carcinoma

value: 15 years

value: ENCBS177XUL at ENCODE; https://www.encodeproject.org/ENCBS177XUL/


title: MPRA from K562 (ENCLB778OVV)

description:
https://www.encodeproject.org/experiments/ENCSR147BIK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147BIK
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB778OVV
fragmentation methods: none

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: ENCBS708UJQ at ENCODE; https://www.encodeproject.org/ENCBS708UJQ/


title: ExVi2Red_01_B02

value: pancreas

value: 4 mpf

value: beta-cell

tag: treatment


title: MPRA from HepG2 (ENCLB722ECI)

description:
https://www.encodeproject.org/experiments/ENCSR167HAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR167HAR
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB722ECI
fragmentation methods: none

value: child

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS963KTX at ENCODE; https://www.encodeproject.org/ENCBS963KTX/


title: ExVi2Red_01_A02

value: photoconversion


title: ExVi2Red_01_C02


title: ExVi2Red_01_E02


title: MPRA from K562 (ENCLB512MVB)

description:
https://www.encodeproject.org/experiments/ENCSR147BIK/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR147BIK
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB512MVB
fragmentation methods: none

value: cell line

value: not applicable

value: ENCBS185DDM at ENCODE; https://www.encodeproject.org/ENCBS185DDM/


title: MPRA from A549 (ENCLB292JQF)

description:
https://www.encodeproject.org/experiments/ENCSR213UGS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR213UGS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR205HWY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB292JQF
fragmentation methods: none

value: male

value: 58 years

tag: passage number

value: ENCBS339TTJ at ENCODE; https://www.encodeproject.org/ENCBS339TTJ/


title: MPRA from K562 (ENCLB043YMC)

description:
https://www.encodeproject.org/experiments/ENCSR147BIK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR147BIK
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB043YMC
fragmentation methods: none

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS305XUX at ENCODE; https://www.encodeproject.org/ENCBS305XUX/


title: ExVi2Red_01_D02

value: pancreas

value: 4 mpf

tag: genotype


title: ExVi2Red_01_F02

value: beta-cell


title: MPRA from K562 (ENCLB142DYB)

description:
https://www.encodeproject.org/experiments/ENCSR147BIK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR147BIK
assay title: MPRA
assembly: hg19
possible controls: ENCSR720LEA
encode release date: 2021-09-10
lab: Ryan Tewhey, JAX
library encode accession: ENCLB142DYB
fragmentation methods: none

tag: line

value: 53 years

value: Ryan Tewhey, JAX

value: ENCBS480PQP at ENCODE; https://www.encodeproject.org/ENCBS480PQP/


title: ExVi2Red_01_G02

value: photoconversion


title: ExVi2Red_01_H02


title: ExVi2Red_01_A03


title: MPRA from K562 (ENCLB382ZNX)

description:
https://www.encodeproject.org/experiments/ENCSR135MRI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR135MRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB382ZNX
fragmentation methods: none

value: cell line

tag: biosample encode accession

value: ATCC

value: ENCBS696VSK at ENCODE; https://www.encodeproject.org/ENCBS696VSK/


title: ExVi2Red_01_B03


title: MPRA from K562 (ENCLB809ZZK)

description:
https://www.encodeproject.org/experiments/ENCSR135MRI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR135MRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB809ZZK
fragmentation methods: none

tag: collection date

value: not applicable

value: ENCBS190NGI at ENCODE; https://www.encodeproject.org/ENCBS190NGI/


title: MPRA from HepG2 (ENCLB091RTO)

description:
https://www.encodeproject.org/experiments/ENCSR167HAR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR167HAR
assay title: MPRA
possible controls: ENCSR020JTL
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB091RTO
fragmentation methods: none

tag: geographic location

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS875QYK at ENCODE; https://www.encodeproject.org/ENCBS875QYK/


title: ExVi2Red_01_C03

value: pancreas


title: MPRA from K562 (ENCLB052JNM)

description:
https://www.encodeproject.org/experiments/ENCSR135MRI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR135MRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB052JNM
fragmentation methods: none

tag: encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS832DVZ at ENCODE; https://www.encodeproject.org/ENCBS832DVZ/


title: MPRA from HepG2 (ENCLB146WYG)

description:
https://www.encodeproject.org/experiments/ENCSR045VPN/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR045VPN
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB146WYG
fragmentation methods: none

tag: Sex

value: Ryan Tewhey, JAX

value: ENCBS163HDT at ENCODE; https://www.encodeproject.org/ENCBS163HDT/


title: MPRA from HepG2 (ENCLB601LGM)

description:
https://www.encodeproject.org/experiments/ENCSR045VPN/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR045VPN
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB601LGM
fragmentation methods: none

value: cell line

tag: dev stage

value: ENCBS345LAQ at ENCODE; https://www.encodeproject.org/ENCBS345LAQ/


title: ExVi2Red_01_E03

tag: age

value: 4 mpf

value: beta-cell

value: photoconversion


title: MPRA from GM12878 (ENCLB674CII)

description:
https://www.encodeproject.org/experiments/ENCSR248ZDI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR248ZDI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB674CII
fragmentation methods: none

value: not applicable

tag: health state

value: unknown

value: ATCC

value: ENCBS869VDM at ENCODE; https://www.encodeproject.org/ENCBS869VDM/


title: ExVi2Red_01_F03


title: MPRA from HepG2 (ENCLB768GAO)

description:
https://www.encodeproject.org/experiments/ENCSR045VPN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045VPN
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB768GAO
fragmentation methods: none

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

tag: lab

value: ENCBS794MPK at ENCODE; https://www.encodeproject.org/ENCBS794MPK/


title: MPRA from HepG2 (ENCLB761HYK)

description:
https://www.encodeproject.org/experiments/ENCSR045VPN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR045VPN
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB761HYK
fragmentation methods: none

tag: source

value: ENCBS767QTF at ENCODE; https://www.encodeproject.org/ENCBS767QTF/


title: MPRA from HepG2 (ENCLB340HIY)

description:
https://www.encodeproject.org/experiments/ENCSR045VPN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR045VPN
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB340HIY
fragmentation methods: none

value: Ryan Tewhey, JAX

tag: link

value: ENCBS543GRY at ENCODE; https://www.encodeproject.org/ENCBS543GRY/


title: ExVi2Red_01_A04

tag: tissue

value: pancreas


title: ExVi2Red_01_C04

tag: cell type


title: MPRA from K562 (ENCLB958VTS)

description:
https://www.encodeproject.org/experiments/ENCSR135MRI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135MRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB958VTS
fragmentation methods: none

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: ENCBS510XNG at ENCODE; https://www.encodeproject.org/ENCBS510XNG/


title: ExVi2Red_01_B04

value: 4 mpf

value: beta-cell

tag: treatment

value: photoconversion


title: MPRA from GM12878 (ENCLB116SRK)

description:
https://www.encodeproject.org/experiments/ENCSR015VGW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR015VGW
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB116SRK
fragmentation methods: none

value: not applicable

value: unknown

tag: passage number

value: ATCC

value: ENCBS364GTE at ENCODE; https://www.encodeproject.org/ENCBS364GTE/


title: MPRA from GM12878 (ENCLB630EAM)

description:
https://www.encodeproject.org/experiments/ENCSR015VGW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR015VGW
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB630EAM
fragmentation methods: none

value: ENCBS974NZF at ENCODE; https://www.encodeproject.org/ENCBS974NZF/


title: MPRA from GM12878 (ENCLB154NOG)

description:
https://www.encodeproject.org/experiments/ENCSR015VGW/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR015VGW
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB154NOG
fragmentation methods: none

value: Ryan Tewhey, JAX

value: ENCBS794CVM at ENCODE; https://www.encodeproject.org/ENCBS794CVM/


title: ExVi2Red_01_E04

value: pancreas

tag: genotype


title: ExVi2Red_01_D04


title: MPRA from K562 (ENCLB323QFZ)

description:
https://www.encodeproject.org/experiments/ENCSR135MRI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR135MRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB323QFZ
fragmentation methods: none

tag: line

value: cell line

value: ENCBS508SLB at ENCODE; https://www.encodeproject.org/ENCBS508SLB/


title: MPRA from GM12878 (ENCLB050OKV)

description:
https://www.encodeproject.org/experiments/ENCSR015VGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR015VGW
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB050OKV
fragmentation methods: none

tag: biosample encode accession

value: female

value: ENCBS274EWD at ENCODE; https://www.encodeproject.org/ENCBS274EWD/


title: MPRA from GM12878 (ENCLB741ROG)

description:
https://www.encodeproject.org/experiments/ENCSR015VGW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR015VGW
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB741ROG
fragmentation methods: none

tag: collection date

value: adult

value: ENCBS639KKF at ENCODE; https://www.encodeproject.org/ENCBS639KKF/


title: ExVi2Red_01_G04

value: 4 mpf


title: ExVi2Red_01_D03

value: beta-cell


title: ExVi2Red_01_F04

value: photoconversion


title: ExVi2Red_01_H04


title: MPRA from K562 (ENCLB728REF)

description:
https://www.encodeproject.org/experiments/ENCSR003TJR/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR003TJR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB728REF
fragmentation methods: none

value: not applicable

tag: geographic location

value: chronic myelogenous leukemia (CML)

value: 53 years

value: ENCBS829TAP at ENCODE; https://www.encodeproject.org/ENCBS829TAP/


title: MPRA from K562 (ENCLB787WCW)

description:
https://www.encodeproject.org/experiments/ENCSR003TJR/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR003TJR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB787WCW
fragmentation methods: none

tag: encode accession

value: ATCC

value: ENCBS950BEX at ENCODE; https://www.encodeproject.org/ENCBS950BEX/


title: MPRA from K562 (ENCLB475QKV)

description:
https://www.encodeproject.org/experiments/ENCSR003TJR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR003TJR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB475QKV
fragmentation methods: none

tag: Sex

value: Ryan Tewhey, JAX

value: ENCBS944MCA at ENCODE; https://www.encodeproject.org/ENCBS944MCA/


title: ExVi2Red_01_G03

value: pancreas


title: ExVi2Red_01_A05


title: ExVi2Red_01_B05


title: ExVi2Red_01_H03


title: MPRA from K562 (ENCLB966KKW)

description:
https://www.encodeproject.org/experiments/ENCSR003TJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR003TJR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB966KKW
fragmentation methods: none

value: cell line

tag: dev stage

value: ENCBS488MDW at ENCODE; https://www.encodeproject.org/ENCBS488MDW/


title: ExVi2Red_01_C05

tag: age


title: Evs-PANC-1-rep3

city: Guangzhou

first: Shangyou

last: Zheng

state: Guangdong

address: Guangzhou

country: China

institute: Guangdong Provincial People's Hospital

data_processing:
Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
Assembly: UCSC HG19
Supplementary files format and content: EXCEL files include all gene expression

extract_protocol:
PANC-1 cells were treated with CAF-derived EVs for 2 weeks and then collected for RNA extraction
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), ribosomal RNA was removed from 1 μg total RNA using Ribo-off® rRNA Depletion Kit (Human/Mouse/Rat, Vazyme, cat.N406-01, Nanjing, China) and purified using VAHTS® RNA Clean Beads (Vazyme, cat. N412, Nanjing, China). VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, cat.NR604-02, Nanjing, China) was used for lncRNA library construction following the manufacturer's protocol. The enriched ncRNAs were segmented with FRAG/PRIME Buffer. The first cDNA strand was generated by reverse transcription starting from -3 ’ , and the second cDNA strand with U was synthesized using the first cDNA strand. Single- or dual-index adapters were ligated to the fragments with ligase, and size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). The ligated products were amplified with PCR by the following conditions: Incubated at 37 ° C for 10 minutes to remove the U containing antisense chain, initial denaturation at 98℃ for 10 sec; 12-14 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, extension at 72℃ for 30 sec, and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 290bp (±50 bp). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Illumina Corporation， San Diego，USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

tag: cell line

value: Pancreatic cancer cells

value: CAFs-EVs


title: UHR_01_E05


title: Evs-PANC-1-rep1


title: PANC-1-rep3


title: ExVi2Red_01_G05


title: ExVi2Red_01_F05


title: PANC-1-rep2


title: PANC-1-rep1


title: ExVi2Red_01_C06


title: ExVi2Red_01_A06


title: NC_01_E06


title: independenttrial_7_38_LiveCD8Tcells_GEX

city: Philadelphia

first: Andy

last: Minn

state: Philadelphia

address: 421 Curie  Blvd

institute: University of Pennsylvania

description:
10x Genomics
Merged_p38_CD8_sorted_and_PBMC_extracted.rds

data_processing:
Sequencing data was processed using CellRanger pipeline v5 (10x Genomics). BCL files were converted to FASTQ and aligned to the human genome (GRCh38) to generate count matrices.
Assembly: GRCh38
Supplementary files format and content: RDS object containing CD8 T cells for both the sorted CD45+ cells and the enriched CD8 T cells libraries.  Cells with >10% mitochondrial DNA, <200 or >2500 RNA features were filtered out and conditions integrated using Seurat v3.2.0. UMI barcodes were used to combine cell expression data with clonotype data.

source_name: PBMCs

extract_protocol:
Cells were stained with Viability and antibodies against CD45 and CD8. Cells were sorted for  Live CD45+ and Live CD8+
Cells were sorted into GEMs using 10x Chromium Controller and were made into libraries following the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) Protocol

value: PBMCs

tag: response

value: independent trial

value: Live CD8+ T cells

tag: time

tag: disease state

value: NSCLC


title: independenttrial_6_69_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p69_CD8_sorted_and_PBMC_extracted.rds

tag: tissue


title: JAKiR_6_27_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p27_CD8_sorted_and_PBMC_extracted.rds

tag: cell type


title: MPRA from K562 (ENCLB615ACM)

description:
https://www.encodeproject.org/experiments/ENCSR003TJR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR003TJR
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB615ACM
fragmentation methods: none

value: not applicable

value: female

tag: health state

value: adult

tag: lab

tag: source

tag: link

value: ENCBS224FLX at ENCODE; https://www.encodeproject.org/ENCBS224FLX/


title: ExVi2Red_01_F06

value: 4 mpf

value: beta-cell

tag: genotype

tag: treatment

value: photoconversion


title: NR_6_25_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p25_CD8_sorted_and_PBMC_extracted.rds

value: NR


title: ExVi2Red_01_H06

value: pancreas


title: independenttrial_5_69_LiveCD8Tcells_GEX


title: ExVi2Red_01_A07


title: ExVi2Red_01_G06


title: independenttrial_3_38_LiveCD8Tcells_GEX


title: NR_5_25_LiveCD8Tcells_GEX


title: JAKiR_4_27_LiveCD8Tcells_GEX


title: ExVi2Red_01_D05


title: NR_2_25_LiveCD8Tcells_GEX


title: ExVi2-30_01_E07


title: ExVi2Red_01_B07


title: Evs-PANC-1-rep2


title: ExVi2Red_01_D06


title: independenttrial_2_69_LiveCD8Tcells_GEX


title: ExVi2Red_01_D07


title: JAKiR_2_27_LiveCD8Tcells_GEX


title: independenttrial_1_38_LiveCD8Tcells_GEX

value: Baseline


title: ExVi2Red_01_A08


title: ExVi2Red_01_B06


title: NR_1_25_LiveCD8Tcells_GEX


title: independenttrial_6_69_LiveCD45PBMCs_GEX

value: Live CD45+ PBMCs


title: independenttrial_7_38_LiveCD45PBMCs_GEX


title: ExVi2Red_01_H07


title: independenttrial_4_38_LiveCD8Tcells_GEX


title: ExVi2Red_01_F07


title: independenttrial_1_69_LiveCD8Tcells_GEX


title: JAKiR_6_27_LiveCD45PBMCs_GEX


title: ExVi2Red_01_E08


title: NR_6_25_LiveCD45PBMCs_GEX


title: ExVi2Red_01_G07


title: ExVi2Red_01_C07


title: ExVi2Red_01_D08


title: JAKiR_1_27_LiveCD8Tcells_GEX


title: ExVi2Red_01_B08


title: ExVi2Red_01_F08


title: independenttrial_4_38_LiveCD45PBMCs_GEX


title: independenttrial_5_69_LiveCD45PBMCs_GEX


title: ExVi2Red_01_A09


title: ExVi2Red_01_C08


title: ExVi2Red_01_B09


title: ExVi2Red_01_G08


title: independenttrial_2_69_LiveCD45PBMCs_GEX


title: NR_5_25_LiveCD45PBMCs_GEX


title: ExVi2Red_01_H08


title: ExVi2Red_01_D09


title: JAKiR_2_27_LiveCD45PBMCs_GEX


title: JAKiR_4_27_LiveCD45PBMCs_GEX


title: independenttrial_1_38_LiveCD45PBMCs_GEX


title: ExVi2Red_01_F09


title: MPRA from A549 (ENCLB588KKT)

description:
https://www.encodeproject.org/experiments/ENCSR213UGS/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR213UGS
assay title: MPRA
assembly: hg19, GRCh38
possible controls: ENCSR205HWY
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB588KKT
fragmentation methods: none

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

tag: geographic location

value: male

value: 58 years

tag: passage number

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS242JBI at ENCODE; https://www.encodeproject.org/ENCBS242JBI/


title: ExVi2Red_01_C09

tag: age


title: NR_1_25_LiveCD45PBMCs_GEX

value: PBMCs

tag: response

value: NSCLC


title: ExVi2Red_01_A10


title: ExVi2Red_01_B10


title: JAKiR_6_12_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p12_CD8_sorted_and_PBMC_extracted.rds

value: Live CD8+ T cells

tag: time


title: ExVi2Red_01_H09


title: NR_2_25_LiveCD45PBMCs_GEX

tag: disease state


title: ExVi2Red_01_C10

tag: tissue


title: JAKiR_1_27_LiveCD45PBMCs_GEX

tag: cell type


title: aPD1R_4_3_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p3_CD8_sorted_and_PBMC_extracted.rds


title: independenttrial_1_69_LiveCD45PBMCs_GEX

value: independent trial


title: JAKiR_2_12_LiveCD8Tcells_GEX


title: JAKiR_4_12_LiveCD8Tcells_GEX


title: ExVi2Red_01_D10

value: 4 mpf


title: ExVi2Red_01_G10

value: beta-cell


title: ExVi2Red_01_G09

value: photoconversion


title: ExVi2Red_01_H10


title: ExVi2Red_01_E09


title: JAKiR_1_12_LiveCD8Tcells_GEX


title: aPD1R_6_3_LiveCD8Tcells_GEX


title: aPD1R_6_3_LiveCD45PBMCs_GEX


title: ExVi2Red_01_E10


title: aPD1R_2_3_LiveCD8Tcells_GEX


title: ExVi2Red_01_F10


title: ExVi2Red_01_A11


title: JAKiR_6_12_LiveCD45PBMCs_GEX


title: aPD1R_1_3_LiveCD8Tcells_GEX


title: ExVi2Red_01_B11


title: ExVi2Red_01_C11


title: JAKiR_4_12_LiveCD45PBMCs_GEX


title: ExVi2Red_01_D11


title: ExVi2Red_01_E11


title: ExVi2Red_01_G11


title: ExVi2Red_01_H11


title: JAKiR_2_12_LiveCD45PBMCs_GEX


title: JAKiR_1_12_LiveCD45PBMCs_GEX


title: aPD1R_2_3_LiveCD45PBMCs_GEX


title: NR_6_7_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p7_CD8_sorted_and_PBMC_extracted.rds

value: NR


title: ExVi2Red_01_C12

value: pancreas


title: aPD1R_6_6_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p6_CD8_sorted_and_PBMC_extracted.rds


title: ExVi2Red_01_B12


title: ExVi2Red_01_F11


title: ExVi2Red_01_D12


title: JAKiR_6_4_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p4_CD8_sorted_and_PBMC_extracted.rds


title: NR_6_13_LiveCD8Tcells_GEX

description:
10x Genomics
Merged_p13_CD8_sorted_and_PBMC_extracted.rds


title: ExVi2Red_01_E12


title: ExVi2Red_01_G12


title: aPD1R_4_6_LiveCD8Tcells_GEX


title: ExVi2Red_01_F12


title: NR_4_7_LiveCD8Tcells_GEX


title: JAKiR_4_4_LiveCD8Tcells_GEX


title: ExVi2Red_01_H12


title: NR_4_13_LiveCD8Tcells_GEX


title: aPD1R_1_3_LiveCD45PBMCs_GEX

value: Baseline


title: aPD1R_4_3_LiveCD45PBMCs_GEX

value: Live CD45+ PBMCs


title: ExVi16Gr_02_A01


title: ExVi2Red_01_A12


title: ExVi16Gr_02_B01


title: aPD1R_2_6_LiveCD8Tcells_GEX


title: JAKiR_2_4_LiveCD8Tcells_GEX


title: NR_2_7_LiveCD8Tcells_GEX


title: ExVi16Gr_02_D01


title: NR_2_13_LiveCD8Tcells_GEX


title: ExVi16Gr_02_C01


title: ExVi16Gr_02_F01


title: aPD1R_1_6_LiveCD8Tcells_GEX


title: ExVi16Gr_02_G01


title: JAKiR_1_4_LiveCD8Tcells_GEX


title: ExVi16Gr_02_H01


title: NR_6_7_LiveCD45PBMCs_GEX


title: NR_1_7_LiveCD8Tcells_GEX


title: ExVi16Gr_02_E01


title: ExVi16Gr_02_B02


title: NR_1_13_LiveCD8Tcells_GEX


title: ExVi16Gr_02_C02


title: ExVi16Gr_02_A02


title: NR_6_13_LiveCD45PBMCs_GEX


title: JAKiR_6_4_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_D02


title: NR_4_7_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_E02


title: ExVi16Gr_02_F02


title: aPD1R_4_6_LiveCD45PBMCs_GEX


title: NR_4_13_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_G02


title: ExVi16Gr_02_B03


title: ExVi16Gr_02_H02


title: ExVi16Gr_02_A03


title: aPD1R_2_6_LiveCD45PBMCs_GEX


title: JAKiR_4_4_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_C03


title: NR_2_7_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_D03


title: aPD1R_6_6_LiveCD45PBMCs_GEX


title: aPD1R_1_6_LiveCD45PBMCs_GEX


title: NR_2_13_LiveCD45PBMCs_GEX


title: NR_1_7_LiveCD45PBMCs_GEX


title: JAKiR_2_4_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_G03


title: ExVi16Gr_02_E03


title: ExVi16Gr_02_F03


title: JAKiR_1_4_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_H03


title: NR_1_13_LiveCD45PBMCs_GEX


title: ExVi16Gr_02_A04


title: ExVi16Gr_02_C04


title: ExVi16Gr_02_D04


title: ExVi16Gr_02_E04


title: ExVi16Gr_02_F04


title: A549 cells, YTHDC1 CLIP-seq rep1

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
Quality filtering and collapsing exact duplicates
Alignment: bwa mem
UMI stripping: UMItools
Collapsing PCR duplicates
Bigwig generation: deeptools bamCoverage
Peak-calling: Piranha
Assembly: hg19
Supplementary files format and content: YTHDC1_CLIP.bw is a bigwig file ready to visualize in a browser
Supplementary files format and content: FA_peaks.bed is a bed files with the peaks called by Piranha

molecule: nuclear RNA

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured in DMEM medium (GIBCO), and maintained at 37ºC in presence of 5% CO2

extract_protocol:
30x106 A549 per condition were crosslinked with 1% formaldehyde in 1X PBS for 10 minutes in agitation. Crosslinking was quenched with final concentration of 125 mM Glycine (Bio-Rad). Cells were fractionated as described by Neugebauer’s lab (Brugiolo et al., 2017). After obtaining chromatin extracts, pellet was sheared by sonication in a Bioruptor device for 5 cycles (30’’ON-30’’OFF). We cleared nuclear extract by centrifugating 30 minutes at max speed and incubation with 50 µL Protein A/G Dynabeads for 1 hour at 4ºC. Chromatin extract was incubated with primary antibodies (Table S4) overnight at 4ºC in rotation. The following day, 50 µL Protein A/G Dynabeads where washed and mixed to antibody-hybridized nuclear extract for 6 hours at 4ºC. Beads were washed following the next order: 1 wash of Low-Salt Buffer (150 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of High-Buffer (500 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of LiCl Buffer (0.25 M LiCl, 1% IGEPAL, 1% Na-Deoxycholate [Na-DOC], 1 mM EDTA, 10 mM Tris [pH 8]) and 2 washes with TE Buffer (10 mM Tris, 1 mM EDTA [pH 8]). Beads are resuspended in 250 µL of Elution Buffer (25 mM Tris [pH 7.5], 5 mM EDTA, 0.5% SDS) supplemented with 10 µL of 5 M NaCl, 10 µL 1M Tris pH 7, 5 uL 0.5 M EDTA and 20 µg Proteinase K for 4 hours at 65ºC to promote proper decrosslinking of chromatin from immunoprecipitated proteins. RNA was isolated with TRI Reagent (Sigma-Aldrich) isolation and resuspended in 50 µL of water. Samples were treated with TURBO DNAse I (Invitrogen) for 45 minutes at 37ºC. After that time, a second RNA extraction with TRI Reagent was performed to removed TURBO DNAse I and final quantification by Qubit4 fluorometer (Invitrogen).
SMARTer® Stranded Total RNA-Seq Kit v3

value: Lung adenocarcinoma

tag: cell line

value: WT


title: ExVi16Gr_02_B04


title: unmod_roi,  second mixing experiment

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description: BD Rhapsody

data_processing:
The mapping, barcode filtering and counting was performed using a custom Snakemake pipeline (https://github.com/imallona/rock_roi_method/) based on STARSolo and featurecounts.tsv.gz. Count matrices were analysed in R.
Index the reference genome with STAR.
Subset reads matching the WTA cell barcodes and map those to the transcriptome (genome plus GTF) using STARsolo. Detected cell barcodes (cells) are filtered in at two levels: first, by matching to the user-provided cell barcode whitelist; and second, by applying the EmptyDrops algorithm to discard empty droplets. We report two outputs from this step: the filtered-in cells according to the aforementioned filters; and the unbiased, whole-transcriptome WTA count table
Subset reads matching both the TSO CB structure and the filtered in cell barcodes and map those to the transcriptome. Our reasoning is that the expected TSO transcriptional complexity is undefined and not usable to tell apart cells from empty droplets, so we borrow the filtered-in cells from the EmptyDrops results from the WTA analysis.
(optional) Count on-target features in a more lenient way, filtering in multioverlapping and multimapping reads. This run mode is recommended when the captured regions target non unique loci (i.e. repetitive sequences)
Assembly: Combined genome, mouse: GRCm38.p6.genome.fa and gencode.vM25.annotation.gtf, human: GRCh38.p13.genome.fa and gencode.v38.basic.annotation.gtf. Additional sequences: eGFP and tdTomato
Supplementary files format and content: STARsolo output files wta: tab-delimited tsv.gz and sparse matrix mtx.gz files; filtered by EmptyDrops barcodes (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz)
Supplementary files format and content: STARsolo output files tso: tab-delimited tsv.gz and sparse matrix mtx.gz files; raw counts (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz)
Supplementary files format and content: tab-delimited featurecounts.tsv.gz table for wta for wta and tso (wta_featurecounts.tsv.gz.tsv.gz, tso_featurecounts.tsv.gz.tsv.gz)
Supplementary files format and content: Bigwig coverage track for wta and tso (tso.bw and wta.bw)
Supplementary files format and content: GTF file containing information on the custom RoCK and ROI regions (custom_regions_mixing.gtf)
Supplementary files format and content: comma-separated table containing information on the species assignment for each cell barcode kept for analysis after doublet removal and QC filtering (species.csv)

source_name: Mix of L-cells and HEK293T cells

growth_protocol: HEK193 cells and L-cells cells were cultured in DMEM 1X with 10% FBS and 1% PIS in a 10 cm dish and maintained in an incubator at 37°C and 5% CO2

extract_protocol:
Cells were dissociated using Trypsin-EDTA, filtered through a cell strainer and resuspended in BD Rhapsody Sample Buffer
Libraries were generated on a BD Rhapsody Express machine. Libraries for unmodified samples (unmod) were generated following manufacturers recommendations for the WTA assay. The protocol for v1 BD Rhapsody was used (i.e. a single RPE reaction) and applied to enhanced beads, either with prior RoCKseq modification (rock, rockroi conditions) or without modification (unmod, unmod_roi). rock, unmod_roi and rockroi conditions were generated following the RoCK and ROI protocol. Briefly, the protocol differs from the standard WTA protocol due to the following points: 1) addtion of N1 primer to the RPE PCR (for unmod_roi, rock and rockroi conditions); 2) addition of ROIseq primers to the pool of randomeres during RPE extension (for unmod_roi and rockroi conditions); 3) separate indexing reaction for the samples in which the N1 primer is added; 4) custom sequencing primer

tag: protocol

value: custom single-cell RNA-seq

value: Mix of L-cells and HEK293T cells

value: Mouse adult adipose, human embryonic kidney


title: Jurkat cells, PMA Ionomycin + 1 uM SP100030, 8 hours, p300

city: Cleveland

first: Yi Fan

last: Chen

state: OH

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

description: p300 antibody

data_processing:
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.5.0.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.4
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.5.2
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files
Library strategy: CUT&RUN

source_name: Peripheral blood mononuclear cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies. Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation.
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions. Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol: Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals) where specified. 1 uM S109, 1 uM SP100030, or 10 uM C646 were co-treated for 8 hours (S109, SP100030) or 24 hours (C646)

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: PMA Ionomycin + SP100030


title: rockroi, second mixing experiment

description: BD Rhapsody


title: unmod, second mixing experiment

description: BD Rhapsody


title: A549 cells, YTHDC1 CLIP-seq rep2


title: ExVi16Gr_02_H04


title: ExVi16Gr_02_G04


title: ExVi16Gr_02_A05


title: Jurkat cells, basal state (no activation), 8 hours, p300 antibody, rep2

description: p300 antibody

value: DMSO


title: N.5.Ctl.oxt

city: TOULOUSE

first: Juliette

last: SALLES

address: CHU Purpan - BP 3028

country: France

institute: INSERM

data_processing:
Sequence reads were trimmed/low quality filtered using trimgalore v. 0.6.4_dev, wrapper of Cutadapt v. 2.8
Trimmed sequence reads were mapped to the GRCh38 genome using STAR v. 2.7.5a
Raw analysis was performed using the R software[1], Bioconductor[2]packages including DESeq2[3,4]and the SARTools package developed at PF2 - Institut Pasteur.
Normalization and differential analysis are carried out according to the DESeq2 model and package.
Assembly: GRCh38 v. 107
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: IPSCs derived dopaminergic neurons

growth_protocol: Primary human fibroblasts from an unaffected control (adult woman) and a PWS patient with the SNORD116 MD were reprogrammed to iPSC using retrovirus reprogramming, Sendai virus reprogramming, or mRNA reprogramming. The control was obtained from the fibroblast of a healthy adult matched for age. The method for inducing the differentiation of iPSC into neurons has been previously described (PMID: 27789403). In brief, iPSC cultures were routinely retained on mouse embryonic fibroblasts (MEFs) (Globalstem) and cultured in human embryonic stem cell (ES) media. iPSC were differentiated into neurons using a modified SMAD inhibition protocol from fibroblasts from patients and control. TH, GIRK2, DRD2, MAP2 and B3TUB, which are makers for dopaminergic neurons from midbrain, were tested to validate the neural differentiation. We performed three differentiation cell lines.

extract_protocol:
Total RNA was extracted from iPSC-derived neurons using Trizol® reagent (Invitrogen), according to the manufacturer’s instructions. The quality and integrity of the obtained RNA were assessed using an Fragment Analyzer (Agilent Technologies) after a denaturing step at 70 °C for 2 minutes.
RNA librairies for RNA sequencing were prepared with Illumina Total RNA with ribo-zero gold depletion kit following the manufacturer's instructions.

treatment_protocol: Neurons were harvested between days 28 and 32 for DNA and RNA extraction.

value: IPSCs derived dopaminergic neurons

value: Control

value: oxytocin


title: ExVi16Gr_02_C05

value: 4 mpf

value: beta-cell

value: photoconversion


title: N.5.MD.oxt

value: SNORD116 MD


title: Jurkat cells, basal state (no activation), 8 hours, p300 antibody, rep1

description: p300 antibody


title: ExVi16Gr_02_B05

value: pancreas


title: N.2.MD.oxt


title: UHR_02_E05


title: ExVi16Gr_02_F05


title: N.4.MD

value: no treatment


title: N.5.MD


title: ExVi16Gr_02_G05


title: ExVi16Gr_02_H05


title: Jurkat cells, PMA Ionomycin, 8 hours, p300

description: p300 antibody

value: WT

value: PMA Ionomycin


title: N.2.MD


title: ExVi16Gr_02_A06


title: ExVi16Gr_02_B06


title: N.1.MD


title: N.5.Ctl


title: ExVi16Gr_02_D06


title: N.2.Ctl


title: ExVi16Gr_02_C06


title: ExVi16Gr_02_D05


title: ExVi16Gr_02_F06


title: N.1.Ctl


title: Jurkat XPO1 C528S cells, 24 hrs, 10 uM C646, p300 antibody [p300_C646_C528S]

data_processing:
library strategy: CUT&RUN-Seq
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.5.0.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.4
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.5.2
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies
Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions.
Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM S109 or 10 uM C646 were co-treated for 8 hours (S109) or 24 hours (C646)

tag: antibody


title: N.4.Ctl


title: NC_02_E06


title: N.2.Ctl.oxt


title: ExVi16Gr_02_A07


title: Jurkat XPO1 C528S cells, 24 hrs, IgG control antibody [IgG_C528S]

value: IgG


title: Jurkat cells, 8 hrs, S109, p300 antibody

data_processing:
library strategy: CUT&RUN
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.5.0.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.4
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.5.2
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

value: Peripheral blood mononuclear cells


title: Jurkat XPO1 C528S cells, 24 hrs, p300 antibody [p300_C528S]

value: Jurkat E6-1


title: Jurkat XPO1 C528S cells, 24 hrs, 10 uM C646, XPO1 antibody [XPO1_C646_C528S]

value: T cells


title: Jurkat cells, 24 hours, C646, p300 antibody


title: ExV16-30_02_E07


title: ExVi16Gr_02_B07


title: Jurkat XPO1 C528S cells, 24 hrs, XPO1 antibody [XPO1_C528S]


title: ExVi16Gr_02_F07


title: ExVi16Gr_02_C07


title: ExVi16Gr_02_G07


title: ExVi16Gr_02_D07


title: Jurkat cells, 8 hrs, XPO1 antibody


title: Jurkat cells, 24 hours, p300 antibody


title: ExVi16Gr_02_H06


title: ExVi16Gr_02_H07


title: Jurkat cells, 24 hrs, IgG control antibody 2


title: Jurkat cells, 8 hrs hours, S109, XPo1 antibody


title: Jurkat cells, 24 hrs, XPO1 antibody


title: Jurkat cells, 24 hrs, p300 antibody


title: ExVi16Gr_02_E08


title: Jurkat cells, 24 hrs, C646, p300 antibody


title: ExVi16Gr_02_B08


title: ExVi16Gr_02_D08


title: Jurkat cells, 24 hrs, C646, XPO1 antibody


title: ExVi16Gr_02_G06


title: ExVi16Gr_02_F08


title: ExVi16Gr_02_C08


title: ExVi16Gr_02_G08


title: Jurkat cells, 24 hrs, IgG control antibody 1


title: Bulk, HEK293T, YTH-E, rep3

city: Beijing

first: Magdalena

middle: Justyna

last: Koziol

address: Science Park Road

institute: Chinese Institute for Brain Researach, CIBR

data_processing:
For m6A-RIP: We required a minimum quality score of 5 at reads positions. adapters were removed using the software Cutadapt. Additionally, the first 10 nucleotides at the 5’ terminus were eliminated due to the presence of potentially low-quality nucleotides. Mapping and alignment were used by Hisat2, followed by peak calling using Macs2. To ensure reads unambiguously mapped in the genome, we further mapped the reads by bowtie2 alignment programs (The mapping parameters for bowtie2: -k 4, with other parameters in default setting.
For bulk-RNA-seq and m6A identification: Fastq files were filtered for low quality reads  and low quality bases were trimmed from the ends of the reads.  Bwa  was used to align the resulting reads. To identify C-to-T and m6A sites, we used an approach as described by Meyer et al. (Meyer, 2019).
For single cell RNA-seq and m6A identification: Filtered barcode matrices obtained from E-YTH and E-YTHmut single cell data were processed by Seurat. The software Bullseye was used to identify m6A sites in single cell sequencing data (Tegowski et al., 2022).
For single cell RNA-seq matrix files were generated
cims files were generated
Assembly: Mouse: mm39; HEK293T: hg38
Supplementary files format and content: For m6A-RIP: m6A peaks
Supplementary files format and content: For bulk-RNA seq: cims files
Supplementary files format and content: For single cell RNA-seq: matrix files

growth_protocol: Mice: Hippocampi were harvested from 3 month old mice. Animals were maintained and processed in accordance with CIBR guidelines. All experimental methods were approved and followed all regulations of the Welfare and Ethics Review Committee for Laboratory Animals. C57BL/6J mice were originally purchase from the Jackson Laboratory, but were made available through CIBR’s animal facility. For HEK293T cells: HEK293T cells were purchased from Beijing Xiehe Cell Bank and cultured at 37ºC with 5% CO2 in DMEM (Dulbecco's Modified Eagle Medium) containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
HEK293T cells were collected and RNA was extracted for downstream processing; For mouse hippocamus collections, hippocampi were dissected 2 weeks after AAV injectsions and RNA was extracted; for single cell analysis, cells were dissociated 2 weeks after AAV injections with using the Adult Brain Dissociation Kit (Miltenyi Biotex no. 130-107-677); for m6A-RIP, a pulldown was performed on RNA using the m6A antibody (Synaptic Systems, 202011), and a matching control input sample was keept.
for any bulk RNA seq: Sequencing libraries were generated from 1-10ng of total RNA from each replicate using the Single Cell Full Length mRNA kit and TruePrep® DNA Library Prep Kit V2 (Illumina), according to the manufacturer’s instructions. For single cell sequencing: Briefly, after hippocampi dissociation, cells were FACS sorted and EGFP positive were collected in ice-cold PBS containing 0.5% BSA. Per sample, 30,000 cells were loaded into a Rhapsody Cartridge (BD) and processed following the manufacturer’s instructions. Subsequently, single cell RNA sequencing libraries were prepared using the Rhapsody WTA kit (BD). For m6A-RIP: SMARTer Stranded Total RNA-Seq Kit v2 (Takara)
for single cells: Rhapsody WTA kit (BD); for bulk: TruePrep® DNA Library Prep Kit V2 (Illumina); for m6-RIP: SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

treatment_protocol: Stereotaxic injections were performed on mice with AAV viruses; HEK293T cells were transduced;

value: wildtype

value: YTH-E expressed


title: ExVi16Gr_02_B09


title: ExVi16Gr_02_A09


title: Bulk, HEK293T, YTH-E, rep2


title: ExVi16Gr_02_A08


title: ExVi16Gr_02_D09


title: Bulk, HEK293T, YTH-E, rep1


title: ExVi16Gr_02_C09


title: ExVi16Gr_02_E09


title: ExVi16Gr_02_F09


title: Bulk, HEK293T, Mut-E, rep2

value: Mut-E expressed


title: Bulk, HEK293T, Mut-E, rep3


title: ExVi16Gr_02_G09


title: Bulk, HEK293T, Mut-E, rep1


title: Bulk, HEK293T, Mock, rep2

value: Mock


title: Bulk, HEK293T, Mock, rep1


title: Bulk, HEK293T, Mock, rep3


title: ExVi16Gr_02_A10


title: ExVi16Gr_02_B10


title: Migragen slide replicate B1

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

data_processing:
library strategy: Visium Spatial Transcriptomics
Raw sequencing data processed using 10x Genomics Space Ranger
Sequences were aligned to human reference GRCh38-2020-A, GENCODE v32/Ensembl 98
Spots within the collagen-I/cell layer that do not contain cells were excluded using Loupe browser (version 6.4.1, 10x Genomics) Manual Alignment Wizard. The resulting JSON files were provided as input to the spaceranger pipeline via the via the--loupe-alignmentargument”
Gene expression quantified using Space Ranger with default settings
UMI-count matrix and image loaded in Seurat object
Assembly: GRCh38-2020-A, GENCODE v32/Ensembl 98
Supplementary files format and content: *.TIFF Brightfield images (10000 x 10264 pixels) of H&E stained cell/collagen-I film captured using 10X objective on a microscope with a color camera
Supplementary files format and content: *json JSON files used for non-cell spots removing
Supplementary files format and content: *rds Seurat objects containing UMI-count matrices and processed images

source_name: MDA-MB-231 human breast cancer cells (ATCC-HTB-26)

growth_protocol: MDA-MB-231 human breast cancer cells embeded in the collagen-I layer at 4x106 cells/mL

extract_protocol:
Cells/collagen-I film is methanol fixed followed by OCT-based treatment to snap freeze
The collagen-I/cell layer was permeabilized for 8 min at 37°C, followed by reverse transcription, second strand synthesis, denaturation and cDNA amplification according to the Visium Spatial Gene Expression user guide (CG000239 Rev F)

treatment_protocol: A pHe 7.4-6.0 gradient using CO2/HCO3--buffered media in the 5% CO2 atmosphere of the environmentally controlled microscope chamber

tag: sample type

value: OCT-frozen cell/collagen-I film

value: pH gradient (6.0-7.4)


title: ExVi16Gr_02_H09

value: 4 mpf

value: beta-cell

tag: genotype


title: Bulk, HEK293T, E-YTH, rep3

tag: treatment

value: E-YTH expressed


title: Migragen slide replicate C1

value: MDA-MB-231 human breast cancer cells (ATCC-HTB-26)


title: ExVi16Gr_02_H08

value: pancreas

value: photoconversion


title: ExVi16Gr_02_C10


title: Bulk, HEK293T, E-YTH, rep2


title: ExVi16Gr_02_D10


title: Migragen slide replicate A1


title: pooled clone sequencing from DNA cloning sample (ENCLB731XPC)

description:
https://www.encodeproject.org/experiments/ENCSR915INT/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR915INT
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB731XPC

organism: synthetic construct

source_name: control

value: DNA cloning sample

value: cloning host

tag: biosample term name

value: synthetic construct

value: 60 days

tag: lab

value: Ryan Tewhey, JAX

tag: Sex

value: not applicable


title: ExVi16Gr_02_E10


title: Ly108+ Nr4a1 KO TIL-3

city: Shanghai

first: Jing

last: Hao

address: South Chongqing Road 227, Huangpu District

department: Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital

institute: Shanghai Immune Therapy Institute

data_processing:
Sequencing raw data filtered by Trim Galore was mapped the mm10 reference genome using Hisat2
gene expression was normalized with edgeR and indicated by FPKM (Fragment Per Kilobases per Million reads)
Differentially expressed genes (DEG) were detected with DESeq2 by at least 1.5-fold change and FDR lower than 0.01
Assembly: mm10
Supplementary files format and content: exls with FPKM values and counts for each sample

organism: Mus musculus

source_name: T cell

extract_protocol:
RNA was extracted from Trizol frozen sample following the protocol of the kit (Magen, R4801-02)
RNA libraries for RNA-seq were prepared by BGI, and the protocol was chosd accoriding to the amount of RNA

treatment_protocol: In vitro samples were re-stimulated with PMA/Ionomycin for 2hrs

value: T cell

value: Nr4a1 KO


title: Bulk, HEK293T, E-YTH, rep1

value: wildtype


title: Bulk, HEK293T, E-Mut, rep3

value: E-Mut expressed


title: pooled clone sequencing from DNA cloning sample (ENCLB030ZWN)

description:
https://www.encodeproject.org/experiments/ENCSR915INT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR915INT
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB030ZWN

tag: biosample encode accession


title: Bulk, HEK293T, E-Mut, rep2


title: Ly108+ Nr4a1 KO TIL-2


title: ExVi16Gr_02_F10


title: Bulk, HEK293T, E-Mut, rep1


title: ExVi16Gr_02_G10


title: Ly108+ Nr4a1 KO TIL-1


title: pooled clone sequencing from DNA cloning sample (ENCLB214PIC)

description:
https://www.encodeproject.org/experiments/ENCSR915INT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR915INT
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB214PIC


title: Ly108+ Nr4a1 WT TIL-3

value: WT


title: pooled clone sequencing from DNA cloning sample (ENCLB240WPJ)

description:
https://www.encodeproject.org/experiments/ENCSR915INT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR915INT
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB240WPJ


title: Bulk, HEK293T, E-APOBEC1, rep2

value: E-APOBEC1 expressed


title: Ly108+ Nr4a1 WT TIL-2


title: ExVi16Gr_02_B11

value: 4 mpf

value: beta-cell


title: Bulk, HEK293T, E-APOBEC1, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB400ZFB)

description:
https://www.encodeproject.org/experiments/ENCSR889TWE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR889TWE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB400ZFB


title: pooled clone sequencing from DNA cloning sample (ENCLB838BBT)

description:
https://www.encodeproject.org/experiments/ENCSR889TWE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889TWE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB838BBT


title: ExVi16Gr_02_C11


title: pooled clone sequencing from DNA cloning sample (ENCLB055MCO)

description:
https://www.encodeproject.org/experiments/ENCSR889TWE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR889TWE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB055MCO


title: Ly108+ Nr4a1 WT TIL-1


title: Bulk, HEK293T, APOBEC1-E, rep3

value: APOBEC1-E expressed


title: Nr4a1 KO-1


title: pooled clone sequencing from DNA cloning sample (ENCLB068HRJ)

description:
https://www.encodeproject.org/experiments/ENCSR915INT/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR915INT
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB068HRJ


title: Bulk, HEK293T, APOBEC1-E, rep2


title: ExVi16Gr_02_E11

value: pancreas


title: Bulk, HEK293T, APOBEC1-E, rep1


title: pooled clone sequencing from DNA cloning sample (ENCLB237TUN)

description:
https://www.encodeproject.org/experiments/ENCSR889TWE/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR889TWE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB237TUN


title: Nr4a1 WT-2


title: ExVi16Gr_02_H10

value: photoconversion


title: Bulk, HEK293T, E-APOBEC1, rep3


title: Nr4a1 KO-2


title: Nr4a1 WT-1


title: pooled clone sequencing from DNA cloning sample (ENCLB175FQH)

description:
https://www.encodeproject.org/experiments/ENCSR889TWE/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR889TWE
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB175FQH

value: DNA cloning sample


title: ExVi16Gr_02_F11


title: pooled clone sequencing from DNA cloning sample (ENCLB404NFI)

description:
https://www.encodeproject.org/experiments/ENCSR866ZYZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR866ZYZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB404NFI

value: cloning host


title: 42MGBA 53-1 replicate 2 [RNA-seq]

city: Boston

first: Wanying

last: Xu

state: MA

address: Karp Family Research Building

department: Hematology

institute: Boston Children's Hospital & Broad Institute

data_processing:
RNA-seq data were aligned to human reference genome (hg19) by using HISAT2, and read counts for each gene are called using featureCounts
The statistical tests for RNA-seq data, normalizing raw data and identifying differentially-expressed genes in this study were derived from a statistical model derived from DESeq2
Assembly: hg19
Supplementary files format and content: For each cell line, the results from DESeq2 is provided

source_name: Brain

growth_protocol: cell lines were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% Pen/Strep at 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using the NEB Next® Ultra™ II RNA Library Prep Kit (NEB)

value: Brain

value: no treatment


title: ExVi16Gr_02_A11


title: ExVi16Gr_02_G11


title: RV-GFP-2

value: RV-GFP infected


title: pooled clone sequencing from DNA cloning sample (ENCLB424XNX)

description:
https://www.encodeproject.org/experiments/ENCSR845WYW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR845WYW
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB424XNX

value: synthetic construct

value: 60 days

value: Ryan Tewhey, JAX

value: not applicable


title: pooled clone sequencing from DNA cloning sample (ENCLB159AFG)

description:
https://www.encodeproject.org/experiments/ENCSR845WYW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR845WYW
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB159AFG


title: 42MGBA 53-1 replicate 1 [RNA-seq]


title: 42MGBA parental replicate 3 [RNA-seq]


title: ExVi16Gr_02_H11


title: RV-GFP-1

value: T cell


title: ExVi16Gr_02_A12


title: ExVi16Gr_02_D11


title: Nr4a1-OV-2

value: Enhanced Nr4a1 expression


title: pooled clone sequencing from DNA cloning sample (ENCLB110AGS)

description:
https://www.encodeproject.org/experiments/ENCSR845WYW/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR845WYW
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB110AGS


title: ExVi16Gr_02_B12


title: Nr4a1-OV-1


title: pooled clone sequencing from DNA cloning sample (ENCLB450DOR)

description:
https://www.encodeproject.org/experiments/ENCSR845WYW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR845WYW
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB450DOR


title: 42MGBA 53-1 replicate 3 [RNA-seq]


title: 42MGBA parental replicate 2 [RNA-seq]


title: 42MGBA parental replicate 1 [RNA-seq]


title: ExVi16Gr_02_C12


title: pooled clone sequencing from DNA cloning sample (ENCLB838MVW)

description:
https://www.encodeproject.org/experiments/ENCSR845WYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR845WYW
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB838MVW


title: H4 88-1 replicate 3 [RNA-seq]


title: Tim-3+ TIL-2

value: WT


title: ExVi16Gr_02_D12

value: 4 mpf


title: pooled clone sequencing from DNA cloning sample (ENCLB758YMH)

description:
https://www.encodeproject.org/experiments/ENCSR836ULU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR836ULU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB758YMH


title: H4 88-1 replicate 1 [RNA-seq]


title: Nr4a1-HA ChIP

data_processing:
Sequence reads shorter than 20bp were filtered out with Trim Galore.
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 and PCR replicates were removed with MarkDuplicates
Only concordantly mapped pairs were kept for further analysis. Peak calling was performed using MACS2 to identify areas of sequence tag enrichment and ChIPseeker was used for peak annotation and visualization
Assembly: mm10
Supplementary files format and content: BigWig for each sample

extract_protocol:
Cells were fixed with 1% formaldehyde at a concentration of 1 million cells/mL. The fixed cells were digested with MNase cocktail (Active Motif) and sonicated.
ChIP-seq libraries were prepared by BGI

tag: chip antibody

value: HA tag (CST,#3724)


title: pooled clone sequencing from DNA cloning sample (ENCLB739ETG)

description:
https://www.encodeproject.org/experiments/ENCSR836ULU/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR836ULU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB739ETG

tag: age


title: Tim-3+ TIL-1


title: Nr4a1RFP+ TIL-2


title: H4 parental replicate 3 [RNA-seq]


title: ExVi16Gr_02_G12

value: beta-cell


title: ExVi16Gr_02_H12

value: pancreas


title: H4 parental replicate 2 [RNA-seq]


title: Nr4a1RFP+ TIL-1


title: pooled clone sequencing from DNA cloning sample (ENCLB967GRT)

description:
https://www.encodeproject.org/experiments/ENCSR836ULU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR836ULU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB967GRT


title: H4 parental replicate 1 [RNA-seq]


title: Nr4a1-HA Input


title: H4 88-1 replicate 2 [RNA-seq]


title: Pool12 HC

city: Donostia

first: Alex

middle: Martínez

last: Ascensión

state: Gipuzkoa

address: P/ Doctor Begiristain

institute: Biogipuzkoa HRI

data_processing:
Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample

source_name: Plasma

extract_protocol:
The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.

value: Plasma

value: HC

value: EV


title: ExVi16Gr_02_E12

value: photoconversion


title: Pool10 HC


title: Pool11 HC


title: 42MGBA 53-1 replicate 2

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only the first 36 bases were used for mapping when reads are longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For Hi-C, we focus on cis-interactions and therefore only keep Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same fragments.
We next split all these reads into three classes based on their strand orientations (same-strand, inward, or outward), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
Then, We map fragment pairs to each anchor pair and focus on these reads within 2Mb.
We estimated a background frequency between any two anchors based on the average reads count of all anchor pairs that have similar lengths, similar gap distance, and visibility. And then, we calculate the expected value of each anchor pair and then estimate the ratio by using raw reads divided by it. Next, we applied DeepLoop to the output in order to remove noise from bias-corrected Hi-C data.
Assembly: hg19
Supplementary files format and content: For each Hi-C, the top300k loop of each cell line is provided.

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer.
Hi-C libraries were generated using the Arima Hi-C+ kit (Arima Genomics) as described in the kit instructions.

value: Brain

tag: restriction enzyme

value: Arima Hi-C+ kit


title: pooled clone sequencing from DNA cloning sample (ENCLB437CJQ)

description:
https://www.encodeproject.org/experiments/ENCSR830AFA/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR830AFA
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB437CJQ

data_processing: See GSM*_README.txt supplementary file linked below

value: DNA cloning sample

value: cloning host

value: synthetic construct


title: ExVi16Gr_02_F12

data_processing:
Raw reads in fastq format were trimmed using trim-galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome, GRCz10, using HISAT2 with default parameters. htseq-count was used to assign reads to exons thus eventually getting counts per gene.
For analysis, cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non-responsive were compared using ROTS with default parameters.  Genes with false-discovery rate (FDR) less than 0.05 were considered as differentially expressed.
For gene ontology (GO) analysis of differentially expressed genes, FishEnrichR was utilized.  As background, genes expressed in at least 5 % of the cells were used.
Assembly: GRCz10
Supplementary files format and content: csv


title: pooled clone sequencing from DNA cloning sample (ENCLB593TOF)

description:
https://www.encodeproject.org/experiments/ENCSR830AFA/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR830AFA
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB593TOF

value: 60 days

value: Ryan Tewhey, JAX

value: not applicable


title: 42MGBA parental replicate 2


title: 42MGBA 53-1 replicate 1


title: Pool9 HC


title: pooled clone sequencing from DNA cloning sample (ENCLB030JBR)

description:
https://www.encodeproject.org/experiments/ENCSR830AFA/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR830AFA
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB030JBR


title: pooled clone sequencing from DNA cloning sample (ENCLB513RVE)

description:
https://www.encodeproject.org/experiments/ENCSR836ULU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR836ULU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB513RVE


title: Hippocampus, WT, Vehicle, 2M

city: Irvine

first: Kim

last: Green

address: 3400 Biological Sciences III

institute: University of California, Irvine

data_processing:
Processing and read map analyses were performed by Novogene Corporation
Assembly: mm10
Supplementary files format and content: .xlsx files contain FPKM for each sample
Supplementary files format and content: .xlsx files contain raw counts for each sample

source_name: Brain, Hippocampus

extract_protocol:
RNA was extracted using RNA Plus Universal Mini Kit (Qiagen)
RNA Libraries were constructed by Novogene Corporation

value: Brain, Hippocampus

value: Wild-type (C57BL/6J)

value: Vehicle


title: Hippocampus, WT, Vehicle, 3M


title: Hippocampus, WT, Vehicle, 4M


title: 42MGBA parental replicate 1


title: Pool8 SPMS

value: SPMS


title: pooled clone sequencing from DNA cloning sample (ENCLB274PUE)

description:
https://www.encodeproject.org/experiments/ENCSR836ULU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR836ULU
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB274PUE


title: Hippocampus, WT, Vehicle, 4F


title: pooled clone sequencing from DNA cloning sample (ENCLB023HXM)

description:
https://www.encodeproject.org/experiments/ENCSR830AFA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR830AFA
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB023HXM


title: Pool7 SPMS


title: H4 88-1 replicate 2


title: Hippocampus, WT, Vehicle, 3F


title: pooled clone sequencing from DNA cloning sample (ENCLB106NGY)

description:
https://www.encodeproject.org/experiments/ENCSR813IVZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR813IVZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB106NGY


title: pooled clone sequencing from DNA cloning sample (ENCLB150VJJ)

description:
https://www.encodeproject.org/experiments/ENCSR830AFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR830AFA
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB150VJJ


title: Pool6 SPMS


title: H4 88-1 replicate 1


title: Hippocampus, WT, Vehicle, 2F


title: H4 parental replicate 2


title: Pool5 SPMS


title: Hippocampus, WT, Vehicle, 1F


title: Hippocampus, WT, Vehicle, 1M


title: pooled clone sequencing from DNA cloning sample (ENCLB315IBU)

description:
https://www.encodeproject.org/experiments/ENCSR813IVZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813IVZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB315IBU


title: Pool4 RRMS

value: RRMS


title: H4 parental replicate 1


title: Hippocampus, 5xFAD, Vehicle, 4M


title: A549 PolII ChIP, siSCR, rep2

data_processing:
Alignment: bwa mem
Bigwig obtention: deeptools bamcoverage
Assembly: hg19
Supplementary files format and content: PolII_siDC1.bw: bigwig of the pooled reads in siYTHDC1 condition
Supplementary files format and content: PolII_siSCR.bw: bigwig of the pooled reads in siSCR condition

extract_protocol:
30x106 A549 cells were crosslinked with 1% formaldehyde in 1X PBS for 10 minutes in agitation. Crosslinking was quenched with final concentration of 125 mM Glycine (Bio-Rad). Cells were collected and incubated in 7 mL of Cell Lysis Buffer (5 mM Tris [pH 8], 85 mM KCl, 0.5% IGEPAL) for 10 minutes at 4ºC in rotation. Nuclear samples was collected by centrigation for 10 minutes at 3000 xg and 4ºC. Pellet was washed in Cell Lysis Buffer without IGEPAL (5 mM Tris [pH 8], 85 mM KCl) and pelleted again. Pellet was resuspended in RIPA Buffer (150 mM NaCl, 50 mM Tris-HCl [pH 7.5], 0.1% SDS, 0.5% Na-Deoxycholate [Na-DOC], 1% Triton X-100) supplemented with 0.1 mM DTT, 1X cOmplete Protease Inhibitor Cocktail (Roche) and 20U/mL RNAsin Ribonuclease Inhibitors (Promega) for 10 minutes in ice. Lysate was dounced and chromatin was sheared by sonication in a Bioruptor device for 45 cycles (30’’ON-30’’OFF). We cleared nuclear extract by centrifugating 30 minutes at max speed and incubation with 50 µL Protein A/G Dynabeads for 1 hour at 4ºC. Nuclear extract was incubated with primary antibodies (see Table antibodies) overnight at 4ºC in rotation. The following day, 50 µL Protein A/G Dynabeads where washed and mixed to antibody-hybridized nuclear extract for 6 hours at 4ºC. Beads were washed following the next order: 1 wash of Low-Salt Buffer (150 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of High-Buffer (500 mM NaCl, 20 mM Tris [pH 8], 2 mM EDTA, 0.1% SDS, 1% Triton x-100), 1 wash of LiCl Buffer (0.25 M LiCl, 1% IGEPAL, 1% Na-Deoxycholate [Na-DOC], 1 mM EDTA, 10 mM Tris [pH 8]) and 2 washes with TE Buffer (10 mM Tris, 1 mM EDTA [pH 8]). Beads are resuspended in 250 µL of Elution Buffer (25 mM Tris [pH 7.5], 5 mM EDTA, 0.5% SDS) supplemented with 10 µL of 5 M NaCl, 10 µL 1M Tris pH 7, 5 uL 0.5 M EDTA and 20 µg Proteinase K for 4 hours at 65ºC to promote proper decrosslinking of chromatin from immunoprecipitated proteins. DNA was isolated with Phenol:Chloroform:isoamyl (25:24:1) alcohol (Sigma-Aldrich) isolation and quantified by Qubit4 fluorometer (Invitrogen)
Custom protocol

treatment_protocol: For the siSCR and siYTHDC1 knockdowns, siRNAs were transfected 48-72 hours at final concentration of 40 nM. siRNA sequences were obtained from previous studies or designed using the “i-Score Designer” and “siDirect v.2” designing tools, and purchased from Sigma

value: Lung adenocarcinoma

value: siSCR


title: pooled clone sequencing from DNA cloning sample (ENCLB915TYD)

description:
https://www.encodeproject.org/experiments/ENCSR813IVZ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR813IVZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB915TYD


title: Hippocampus, 5xFAD, Vehicle, 3M


title: Pool3 RRMS

value: Plasma

value: EV


title: pooled clone sequencing from DNA cloning sample (ENCLB692CDS)

description:
https://www.encodeproject.org/experiments/ENCSR813IVZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR813IVZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB692CDS


title: pooled clone sequencing from DNA cloning sample (ENCLB909HVS)

description:
https://www.encodeproject.org/experiments/ENCSR798ALS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR798ALS
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB909HVS


title: A549 PolII ChIP, siYTHDC1, rep1


title: Pool2 RRMS


title: A549 PolII ChIP, siSCR, rep1


title: Hippocampus, 5xFAD, Vehicle, 4F


title: Hippocampus, 5xFAD, Vehicle, 2M